Variant report

Variant	rs2037036
Chromosome Location	chr4:90042432-90042433
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:90031396..90034227-chr4:90041663..90045608,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TIGD2-4	chr4:90042215-90044000	NONHSAT097383

Variant related genes	Relation type
ENSG00000271359	Chromatin interaction
ENSG00000138640	Chromatin interaction
ENSG00000180346	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10009665	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10516828	0.84[CHD][hapmap]
rs11097214	0.92[ASN][1000 genomes]
rs11097215	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12509747	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12641645	0.86[ASN][1000 genomes]
rs12643834	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12644568	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12646713	0.92[ASN][1000 genomes]
rs12646734	0.92[ASN][1000 genomes]
rs13124770	0.92[ASN][1000 genomes]
rs13138280	0.81[TSI][hapmap]
rs13148714	0.86[ASN][1000 genomes]
rs1355835	0.86[ASN][1000 genomes]
rs1355838	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1513821	0.85[ASN][1000 genomes]
rs1533291	0.89[JPT][hapmap];0.82[TSI][hapmap]
rs1708661	0.89[JPT][hapmap]
rs1708674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1708678	0.89[JPT][hapmap];0.80[TSI][hapmap]
rs1708684	0.89[JPT][hapmap];0.82[TSI][hapmap]
rs17770293	0.84[CHD][hapmap]
rs1795721	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1795731	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1795732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1795733	0.89[JPT][hapmap];0.82[TSI][hapmap]
rs2037037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458545	0.89[JPT][hapmap]
rs2464517	0.85[ASN][1000 genomes]
rs2670624	0.89[JPT][hapmap];0.82[TSI][hapmap]
rs2670625	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2670626	0.89[JPT][hapmap];0.82[TSI][hapmap]
rs2670629	0.89[JPT][hapmap]
rs2670630	0.89[JPT][hapmap]
rs2704597	0.85[ASN][1000 genomes]
rs2869987	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2869988	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2869990	0.86[ASN][1000 genomes]
rs4634189	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4693221	0.82[ASN][1000 genomes]
rs4693983	0.88[ASN][1000 genomes]
rs6532094	0.89[JPT][hapmap]
rs6532099	0.81[ASN][1000 genomes]
rs6532109	0.85[ASN][1000 genomes]
rs6532112	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6833401	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6833424	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6833576	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6835031	0.88[ASN][1000 genomes]
rs6844490	0.88[ASW][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.89[AFR][1000 genomes]
rs6854285	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72665891	0.85[ASN][1000 genomes]
rs7440590	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs756175	0.88[ASN][1000 genomes]
rs756176	0.88[ASN][1000 genomes]
rs7660709	0.94[GIH][hapmap]
rs7691983	0.92[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7696844	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs938264	0.88[ASN][1000 genomes]
rs938268	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9991151	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2037036	FAM190A	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90033400-90048200	Weak transcription	Ovary	ovary
2	chr4:90033400-90049200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:90033600-90043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:90033600-90045600	Weak transcription	Esophagus	oesophagus
5	chr4:90033600-90045600	Weak transcription	Pancreas	Pancrea
6	chr4:90033600-90049200	Weak transcription	Gastric	stomach
7	chr4:90033600-90052200	Weak transcription	Aorta	Aorta
8	chr4:90034000-90044000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:90034200-90044000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:90034400-90043000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:90034400-90044000	Weak transcription	Brain Substantia Nigra	brain
12	chr4:90034800-90049200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:90035000-90043600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:90035200-90042600	Weak transcription	Fetal Intestine Small	intestine
15	chr4:90035200-90042600	Weak transcription	K562	blood
16	chr4:90035400-90044600	Weak transcription	Fetal Muscle Leg	muscle
17	chr4:90035600-90043600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:90035600-90044000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:90036600-90044800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:90037000-90046200	Weak transcription	Primary T cells from cord blood	blood
21	chr4:90039200-90042800	Weak transcription	HepG2	liver
22	chr4:90039200-90044600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:90039800-90043400	Weak transcription	Placenta	Placenta
24	chr4:90039800-90043800	Weak transcription	Liver	Liver
25	chr4:90040600-90042800	Enhancers	A549	lung
26	chr4:90041000-90043200	Weak transcription	HMEC	breast
27	chr4:90041200-90042600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:90041200-90043200	Weak transcription	NHEK	skin
29	chr4:90041400-90043800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:90041600-90043000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:90041600-90044000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:90041600-90044000	Weak transcription	NH-A	brain
33	chr4:90041600-90045200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:90042200-90047600	Enhancers	Fetal Intestine Large	intestine
35	chr4:90042400-90044800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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